In [1]:
%run preparation.py
%matplotlib inline
In [2]:
HTML('''<script>
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<h3>Actin grinding velocity analysis</h3><br># Prepared by Sam., Prof. Nitta Lab.<br># Click <a href="javascript:code_toggle()">HERE</a> to toggle on/off the raw input code.''')
Out[2]:

Actin grinding velocity analysis


# Prepared by Sam., Prof. Nitta Lab.
# Click HERE to toggle on/off the raw input code.
In [3]:
Dx_tip = np.diff(bmd01['x']); Dy_tip = np.diff(bmd01['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm01, label='Change in binding motor')
#ax1.axhline(float(bm01.mean()), linestyle='--')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.1]', fontdict=font)
plt.grid()

plt.show()
fig.savefig('actin_binding_grinding_r0.1.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 0.4881310002381701
VSD: 0.347930048255116
In [4]:
Dx_tip = np.diff(bmd02['x']); Dy_tip = np.diff(bmd02['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm02, label='Change in binding motor')
#ax1.axhline(float(bm01.mean()), linestyle='--')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.2]', fontdict=font)
plt.grid()

v1 = v.reshape(150,1)
v1 = pd.DataFrame(v1)
tym = pd.DataFrame(time)
bm02_ = bm02.reset_index(drop=True)
nbm02 = pd.concat([tym, bm02_, v1], axis=1)
nbm02 = nbm02.loc[nbm02['b_m'] >= 22] # detached number
#print(nbm02)
nbm02 = nbm02.iloc[:,2]
#print(nbm02)
nbm02 = nbm02[0:21]
#print(nbm02)

plt.show()
fig.savefig('actin_binding_grinding_r0.2.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))
print(colored('Mean velocity, time[0:40] = ', 'yellow', attrs=['reverse', 'blink']), \
      colored(nbm02.mean(), 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 1.838967431564482
VSD: 1.59175989571884
Mean velocity, time[0:40] =  2.365512705927455
In [5]:
Dx_tip = np.diff(bmd03['x']); Dy_tip = np.diff(bmd03['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm03, label='Change in binding motor')
#ax1.axhline(float(bm01.mean()), linestyle='--')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.3]', fontdict=font)
plt.grid()

v1 = v.reshape(150,1)
v1 = pd.DataFrame(v1)
tym = pd.DataFrame(time)
bm03_ = bm03.reset_index(drop=True)
nbm03 = pd.concat([tym, bm03_, v1], axis=1)
nbm03 = nbm03.loc[nbm03['b_m'] >= 2] # detached number
#print(nbm03)
nbm03 = nbm03.iloc[:,2]
#print(nbm03)
nbm03 = nbm03[0:7]
#print(nbm03)

plt.show()
fig.savefig('actin_binding_grinding_r0.3.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))
print(colored('Mean velocity, time[0:12] = ', 'yellow', attrs=['reverse', 'blink']), \
      colored(nbm03.mean(), 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 14.260601379455629
VSD: 10.085729320666001
Mean velocity, time[0:12] =  2.1077852826307453
In [6]:
Dx_tip = np.diff(bmd04['x']); Dy_tip = np.diff(bmd04['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm04, label='Change in binding motor')
#ax1.axhline(float(bm01.mean()), linestyle='--')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.4]', fontdict=font)
plt.grid()

v1 = v.reshape(150,1)
v1 = pd.DataFrame(v1)
tym = pd.DataFrame(time)
bm04_ = bm04.reset_index(drop=True)
nbm04 = pd.concat([tym, bm04_, v1], axis=1)
nbm04 = nbm04.loc[nbm04['b_m'] >= 2] # detached number
#print(nbm04)
nbm04 = nbm04.iloc[:,2]
#print(nbm04)
nbm04_1 = nbm04[0:9]
nbm04_2 = nbm04.iloc[-25:]
#print(nbm04_1)
#print(nbm04_2)

plt.show()
fig.savefig('actin_binding_grinding_r0.4.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))
print(colored('Mean velocity, time[0:16] = ', 'yellow', attrs=['reverse', 'blink']), \
      colored(nbm04_1.mean(), 'yellow', attrs=['reverse', 'blink']))
print(colored('Mean velocity, time[140:189] = ', 'yellow', attrs=['reverse', 'blink']), \
      colored(nbm04_2.mean(), 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 14.079385420413336
VSD: 8.705217389361648
Mean velocity, time[0:16] =  5.693350061033846
Mean velocity, time[140:189] =  11.390969104254467
In [7]:
Dx_tip = np.diff(bmd05['x']); Dy_tip = np.diff(bmd05['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm05, label='Change in binding motor')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.5]', fontdict=font)
plt.grid()

v1 = v.reshape(150,1)
v1 = pd.DataFrame(v1)
tym = pd.DataFrame(time)
bm05_ = bm05.reset_index(drop=True)
nbm05 = pd.concat([tym, bm05_, v1], axis=1)
nbm05 = nbm05.loc[nbm05['b_m'] >= 2] # detached number
#print(nbm05)
nbm05 = nbm05.iloc[:,2]
#print(nbm05)
nbm05_1 = nbm05[0:16]
#nbm05_2 = nbm05.iloc[-25:]
#print(nbm05_1)
#print(nbm05_2)

plt.show()
fig.savefig('actin_binding_grinding_r0.5.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))
print(colored('Mean velocity, time[0:30] = ', 'yellow', attrs=['reverse', 'blink']), \
      colored(nbm05_1.mean(), 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 15.213626963857399
VSD: 8.759060846123349
Mean velocity, time[0:30] =  10.303290288043137
In [8]:
Dx_tip = np.diff(bmd06['x']); Dy_tip = np.diff(bmd06['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm06, label='Change in binding motor')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.6]', fontdict=font)
plt.grid()

v1 = v.reshape(150,1)
v1 = pd.DataFrame(v1)
tym = pd.DataFrame(time)
bm06_ = bm06.reset_index(drop=True)
nbm06 = pd.concat([tym, bm06_, v1], axis=1)
nbm06 = nbm06.loc[nbm06['b_m'] >= 2] # detached number
#print(nbm06.iloc[-104:])
nbm06 = nbm06.iloc[:,2]
#print(nbm06[25:50])
nbm06_1 = nbm06[0:36]
nbm06_2 = nbm06.iloc[-104:]
#print(nbm06_1)
#print(nbm06_2)

plt.show()
fig.savefig('actin_binding_grinding_r0.6.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))
print(colored('Mean velocity, time[0:70] = ', 'yellow', attrs=['reverse', 'blink']), \
      colored(nbm06_1.mean(), 'yellow', attrs=['reverse', 'blink']))
print(colored('Mean velocity, time[92:300] = ', 'yellow', attrs=['reverse', 'blink']), \
      colored(nbm06_2.mean(), 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 11.165640708575953
VSD: 5.2262759614288
Mean velocity, time[0:70] =  10.52988460478295
Mean velocity, time[92:300] =  10.824569433056052
In [9]:
Dx_tip = np.diff(bmd07['x']); Dy_tip = np.diff(bmd07['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm07, label='Change in binding motor')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.7]', fontdict=font)
plt.grid()

plt.show()
fig.savefig('actin_binding_grinding_r0.7.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 9.846827449674283
VSD: 3.769588558986583
In [10]:
Dx_tip = np.diff(bmd08['x']); Dy_tip = np.diff(bmd08['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm08, label='Change in binding motor')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.8]', fontdict=font)
plt.grid()

plt.show()
fig.savefig('actin_binding_grinding_r0.8.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 9.678932420908296
VSD: 4.299344042740472
In [11]:
Dx_tip = np.diff(bmd09['x']); Dy_tip = np.diff(bmd09['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm09, label='Change in binding motor')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 0.9]', fontdict=font)
plt.grid()

plt.show()
fig.savefig('actin_binding_grinding_r0.9.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 9.249774043921864
VSD: 3.970895411482542
In [12]:
Dx_tip = np.diff(bmd10['x']); Dy_tip = np.diff(bmd10['y'])
DD=np.sqrt((Dx_tip**2)+(Dy_tip**2))
v=DD/(2*dt); Av_vel = np.mean(v)
vSD=np.sum(((v-Av_vel)**2)/(np.size(v)-1)); vSD=np.sqrt(vSD)
time = np.linspace(0,300,150)

fig, ax1 = plt.subplots(figsize=(8,6), dpi=500)
ax1.set_xlabel('Time', fontdict=font)
ax1.set_ylabel('Number of binding motors', fontdict=font)
ax1.plot(time,bm10, label='Change in binding motor')
ax1.legend(loc='upper left')

ax2 = ax1.twinx()
ax2.set_xlabel('Time', fontdict=font)
ax2.set_ylabel('Velocity ($\mu m/sec$)', fontdict=font)
ax2.plot(time,v, 'g', label='Change in velocity')
ax2.axhline(np.mean(v), linestyle='--', color='g', label='Mean velocity')
ax2.legend(loc='upper right')
ax2.tick_params('y', colors='g')

plt.title('Binding motors [R = 1.0]', fontdict=font)
plt.grid()

plt.show()
fig.savefig('actin_binding_grinding_r1.0.svg',bbox_inches='tight', format='svg')

print(colored('Ave_vel:', 'yellow', attrs=['reverse', 'blink']), \
      colored(Av_vel, 'yellow', attrs=['reverse', 'blink']))
print(colored('VSD:', 'yellow', attrs=['reverse', 'blink']), \
      colored(vSD, 'yellow', attrs=['reverse', 'blink']))

Ave_vel: 9.063924176283665
VSD: 2.864880289093797
In [ ]: